"After a meeting of the Executive Committee this afternoon I made a decision to resign as President of the Ghana Football Association (GFA)", he said in a statement.
The under coveer journalists also busted 77 Ghanaian referees and 14 Ghana Football Association (GFA) officials allegedly engaging in acts of corruption.
"Government is shocked and outraged at the contents of the recently-aired video documentary, which captures the investigation conducted into football administration by the journalist, Anasa Aremeyaw, titled "Number 12': When Misconducted and Greed become the Norm", the statement read".
The football chief said "scammers" had "deceived me into thinking they were genuine persons interested in investing in our country".
In the said video, Nyantakyi was seen extorting monies from investors by using the name of the President. The Ghana Football Association issued a statement last month backing their president and saying he was innocent until proven guilty.
He also apparently tried to profit personally from a $5 million-a-year, five-year sponsorship deal with the GFA in what the expose said was a "clear breach" of ethics.
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"Government will soon announce provisional measures to govern football activity in the country until a new body is duly formed".
Nyanyakyi's resignation means the Ghana Football Association are now without a president and a vice president after George Afriyie was sacked from his post a month ago.
Federation Internationale de Football Association has not yet commented on whether any action will be taken over the GFA's dissolution.
BBC African football analyst Nick Cavell says it seems unlikely that Ghana will be able to take part in Wednesday's vote for the next host of the 2026 World Cup.
"I wish to apologise to my family, work colleagues, friends, associates and the people of Ghana for the disappointment my indiscretion has caused them". Nyantakyi also has a role within FIFA's council, who are believed to be monitoring the situation.